1640s, "belonging or pertaining to a schismatic sect," applied by Presbyterians to Independents, from Medieval Latin sectarius, from secta "religious group, sect in philosophy or religion" (see sect). By 1796 as "of or pertaining to sects or to attachment to a particular sect; including the tenets of a sect," hence "bigotedly attached to a sect." Sectarial (1816) is "Chiefly used with reference to Indian religions" [OED].
As a noun, "one of a sect" (1650s), especially "one who attaches excessive importance to a sect." The older word in this sense is sectary.
1660s, "characterized by broad-mindedness," especially in reference to 17c. Episcopal clergymen indifferent to doctrinal details; a pseudo-Latin construction from latitude in its meaning "freedom from narrow restrictions" (c. 1600) + ending as in sectarian, etc. Also as a noun from 1660s. Related: Latitudinarianism "liberality of opinion in religion" (1670s); earlier in that sense was latitudinism (1660s).
The awkward derivative episcopalianism, seems to be used for episcopacy, a good English word, which was quite sufficient for the purposes of our honest forefathers, who were strangers to this ridiculous innovation. The word complained of is also reprehensible on the ground of its sectarian termination. ["On the Terms Episcopalian and Episcopalianism," in The Gospel Advocate, October 1821]